Benchmarks of the 3-step pipeline on NA12878 exome (Support protocol 3).

In elPrep, the combined execution of all three preparation steps is faster than running the steps one after the other. Compared to Basic protocol 1 (Table 1), the extra step in this pipeline does not add an additional runtime cost when combining the execution of the steps with elPrep. elPrep executes the full pipeline five to seven times faster than using Picard, depending on how much RAM elPrep can use, namely the same amount as Picard (third column) or all available RAM (fourth column).
Benchmarks of the 3-step pipeline on NA12878 exome (Support protocol 3).